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Table 4 Comparison of geneset differential expression analysis method performances, based on the simulation model proposed by M Ackerman

From: Functional Analysis: Evaluation of Response Intensities - Tailoring ANOVA for Lists of Expression Subsets

   Cut-Off   a2.fixed faeri.
fixed.null
faeri.
fixed.perms
GSA.
mean*
GSA.
absmean*
GSA.
maxmean*
Globaltest.
asymptotic
Globaltest.
gamma
Globaltest.
permutations
Gsea.
pval
Gsea.
fdr
Samgs.
pval
Samgs.
qval
   0.001 Set3 0 0 0 0 0 0 0 0 0 0 0 0 1
H 0   0.01 Set3 1 0 0 0 0 0 0 0 0 0 0 0 2
   0.1 Set3 3 3 3 12 0 0 2 5 3 2 1 2 27
   0.001 Set2 100 96 97 15 25 12 54 96 95 69 20 91 94
  100% DE 0.01 Set2 100 99 99 15 25 12 95 99 97 99 77 98 99
Uni   0.1 Set2 100 100 100 78 72 64 99 99 99 100 100 99 100
   0.001 Set5 72 40 36 0 2 0 3 64 49 14 2 39 56
  50% DE 0.01 Set5 89 75 78 0 2 0 42 89 84 42 25 81 84
   0.1 Set5 100 94 94 7 17 3 93 99 98 93 84 96 99
   0.001 Set1 86 62 60 1 2 2 1 10 8 2 0 7 13
  100% DE 0.01 Set1 89 69 70 1 2 2 20 35 25 16 3 23 41
Uni+Cor   0.1 Set1 95 80 80 11 23 11 58 59 58 46 47 56 73
   0.001 Set4 55 43 39 0 0 0 0 15 7 4 3 4 11
  50% DE 0.01 Set4 65 52 54 0 0 0 18 30 24 13 14 23 43
   0.1 Set4 81 65 65 1 13 1 56 60 57 43 47 56 73
   0.001 Set7 0 100 100 1 67 40 100 100 100 1 0 100 100
  100% DE 0.01 Set7 0 100 100 1 67 40 100 100 100 10 1 100 100
Bidir   0.1 Set7 6 100 100 22 98 82 100 100 100 69 32 100 100
   0.001 Set9 0 84 82 0 7 2 32 95 93 0 0 86 93
  50% DE 0.01 Set9 0 95 95 0 7 2 93 100 100 1 0 100 100
   0.1 Set9 9 100 100 16 48 15 100 100 100 27 8 100 100
   0.001 Set6 0 84 84 0 11 8 5 28 17 6 1 15 25
  100% DE 0.01 Set6 0 88 89 0 11 8 39 50 43 17 8 43 61
Bidir+Cor   0.1 Set6 2 93 93 35 49 54 79 79 78 57 42 78 88
   0.001 Set8 0 63 62 0 2 1 3 30 14 0 0 13 23
  50% DE 0.01 Set8 0 75 76 0 2 1 36 50 42 3 0 40 58
   0.1 Set8 3 86 86 28 27 12 75 78 75 31 15 76 85
  1. Each set of measurements presented was generated 100 times. The measurements in the table show, for each method, the number of detections of the different sets of measurements defined. The upper part of the table presents the results for unidirectional genesets only (all members over expressed) and the lower part concerns groups with a simulated mixed answer (over and under expression). The data related to H0 shows the number of genesets detected by chance (false positives).